Detection of imprinted QTL in the Berkshire x Yorkshire cross

Transcription

1 Detection of imprinted in the Berkshire x Yorkshire cross Jack Dekkers, Hauke Thomsen, Hakkyo Lee 1, Massoud Malek, and Max Rothschild Department of Animal Science and Center for Integrated Animal Genomics 225 Kildee Hall, Iowa State University Ames, IA, 50011, USA 1 National Livestock Research Institute, Suwon, Korea Introduction Genome scans have enabled the detection of regions on chromosomes that contain genes that affect economic traits, so-called quantitative trait loci (). An example is the genome scan that was conducted at ISU in an F 2 cross between the Berkshire and Yorkshire breeds (Malek et al. 2001a,b). This study identified many related to growth performance and meat quality. But this analysis only considered with a Mendelian mode of expression. This implies that an effect of the Berkshire allele on the trait was assumed to be the same whether it was inherited from the F 1 sire or from the F 1 dam (see Figure 1). As a result, the two heterozygotes (BY and YB) are assumed to have the same effect (d). There is, however, evidence that the expression of some genes depends on their parental origin. For example, with paternal expression, a Berkshire gene for increased meat quality would only be expressed in the F 2 progeny if it was inherited from the sire (Figure 2). In that case, individuals with genotype BB and BY are expected to have the same genetic value (Figure 2), as do individuals with genotypes YB and YY. The inheritance mechanism for maternal expression is illustrated in Figure 3. In this case, genotype BB has the same value as YB, as do BY and YY. Figure 1. Mendelian expression. F 0 2 Berkshire sires 9 Yorkshire dams BB x YY Figure 2. Paternal expression. F 0 2 Berkshire sires 9 Yorkshire dams BB x YY F 1 8 sires BY x BY 26 dams F 1 8 sires BY x BY 26 dams F BB BY YB YY Genetic value +a d d -a F BB BY YB YY Genetic value +a +a -a -a

2 The phenomenon of parent-specific expression of genes, and silencing (i.e. nonexpression) of alleles received from the other parent, is referred to as genomic imprinting and has been identified in several mammalian species. Methylation of DNA in specific regions of the genome during formation of gametes by either the sire or the dam has been proposed as one of the main mechanisms for gametic imprinting (Constancia et al., 1998). Methylation of a chromosomal region results in silencing of that region in the progeny because of the inability to transcribe the DNA. To illustrate, in Figure 4 is a situation where a chromosomal region is methylated during gamete formation (meiosis) in the sire but not the dam. Methylation patterns are maintained during regular cell division and development in the progeny and results in silencing of alleles inherited from the sire, i.e. maternal-only expression. Methylation patterns are erased when the progeny itself produces gametes and reinstated depending on the sex of the progeny. Figure 3. Maternal Expression F 0 2 Berkshire sires 9 Yorkshire dams BB x YY F 1 8 sires BY x BY 26 dams Figure 4. Proposed mechanism for gametic Imprinting by DNA methylation (after Constancia et al. 1998) + ~ Gametes Embryo p + m - Somatic tissues p + m - READING F BB BY YB YY Genetic value +a -a +a -a Germline - ERASURE ESTABLISHMENT Generation one Germline MAINTENANCE ERASURE Generation two A limited number of examples for gametic imprinting effects in livestock have been described. De Vries et al. (1994) found evidence for population genetic variance associated with gametic imprinting in three pig populations for growth rate and backfat thickness. Knott et al. (1998) were the first to search for imprinted in a genome scan. They inferred imprinting when effects differed significantly from Mendelian expression. Jeon et al. (1999) and Nezer et al. (1999) found paternal expression for muscularity in the IGF2 region of chromosome 2 in pigs. De Koning et al. (2000, 2001) modified the approach of Knott et al. (1998) and reported a large number of imprinted for growth and meat quality traits in pigs. It should be noted that since imprinting can not be confirmed without further functional tests we will refer to all possible cases of imprinting as parent of origin effects. The purpose of this study was to further analyze the Berkshire-Yorkshire cross data to identify parent of origin effects or imprinted. Materials and Methods The data on the Berkshire x Yorkshire F 2 cross, as described by Dekkers et al. (these proceedings), was used. Detection of with gametic imprinting requires the ability to identify the parental origin (i.e. F 1 dam or sire) of chromosomal regions in the F 2, i.e.

3 genotypes BY and YB must be distinguished. This can be done based on marker data if the F 1 sire and dam have different marker genotypes, as illustrated in Figure 5. Figure 5. Using markers to trace parental origin. Figure 6. Mendelian and parent-of-origin models. Tracing Parental Origin Gametic imprinting and mapping F0 2 Berkshire sires 9 Yorkshire dams BB x YY M 1 N 1 M 3 N 3 Sire BY X BY Dam M 2 N 2 M 4 N 4 F1 8 sires BY x BY 26 dams Progeny BB BY YB YY M 1 N 1 M 3 N 3 F BB BY YB YY M 2 N 2 M 4 N 4 Full model a p +a m a p -a m +d -a p +a m +d -a p -a m Mend. a p =a m = 1 / 2 a +a d d - a M 1 N 1 M 1 N 1 M 3 N 3 M 3 N 3 Pat. Expr. a m =d=0 +a p +a p - a p - a p M 2 N 2 M 4 N 4 M 2 N 2 M 4 N 4 Mat. Expr. a p =d=0 +a m - a m +a m - a m Thus, using marker data, probabilities of parental and breed origin of alleles were derived for each individual in the F 2 generation at every 1-cM position along the genome based on multi-marker data. These probabilities were then used to fit four alternative gene expression models at each 1-cM position, as illustrated in Figure 6: Full model (Full): both parental alleles are expressed but at different levels. Mendelian model (Men): both the parental alleles are expressed and at equal levels. Paternal expression model (Pat): only the paternal allele is expressed. Maternal expression model (Mat): only the maternal allele is expressed. To identify and to determine their mode of inheritance, the alternative models were tested against each other in a sequence of tests following the decision tree in Figure 7. Statistical tests were based on an F-statistic that compared the reduced model to the larger model were used at each point in the decision tree. Significance thresholds for each test were derived using specialized permutation tests. The rationale behind the sequence of tests conducted in the decision tree of Figure 7 is that Mendelian expression can be considered the a priori model for gene expression and that parent-of-origin effects should be inferred only if the effect of the maternal and paternal alleles are significantly different from each other within the region.

4 Results Details on for which parent-of-origin effects were detected are in Table 1. A total of 33 with parent-of-origin effects were detected at the 5% chromosome-wise level, of which 11, 6, and 9 were significant at the 1% chromosome-wise, and at the 5 and 1% genome-wise levels based on their inferred mode of expression. All but twelve of these were not detected by the Mendelian model. Figure 7. Decision tree to identify and determine their mode of inheritance. Men/Null is a test of the Mendelian expression model against a model with no, and is used to detect. All tests of significance were conducted using 5% chromosomewise levels. No Men/Null Significant? Yes Mendelian is base model Full/Null Full/Men No No Significant? Yes Imprinting a pat =a mat Significant? No Mendelian Full/Pat Full/Mat Not signif. significant a mat = 0 Paternal significant Not signif. a pat = 0 Maternal significant Not signif. significant Not signif. Partially imprinted The central region of SSC1 showed evidence of a paternally expressed, most likely pleiotropic, with effects on backfat traits and on loineye area (Table 1). Paternally expressed were detected at the proximal end of chromosome 2 for backfat traits and loineye area. This region is known to contain the IGF2 gene, which has been shown previously to be paternally expressed (Nezer et al. 1999, Jeon et al. 1999, Georges et al. 2003). Two maternally expressed were detected in the distal part of SSC2 for reflectance and ph in the loin.

5 Table 1. with evidence of parent-of-origin effects at the 5% chromosome-wise level. Chr. Trait position Mode of expression Significance Effect estimate b 1 Average backfat 43 Paternal **** Last rib backfat (cm) 41 Paternal **** Tenth rib backfat (cm) 42 Paternal ** Loineye area (cm) ) 39 Paternal ** Average backfat 2 Paternal **** Tenth rib backfat (cm) 5 Paternal **** Lumbar backfat (cm) 4 Paternal **** Last rib backfat (cm) 2 Paternal **** Loineye area (cm) ) 8 Paternal **** h Loin Hunter 135 Maternal * h Loin ph 136 Maternal *** Off flavor score 72 Paternal ** Carcass yield 133 Paternal **** Drip loss 29 Paternal ** Lipid % 128 Maternal * Drip loss 93 Maternal ** h Loin Hunter 95 Maternal *** h Loin Minolta 95 Maternal ** Off flavor score 93 Maternal *** Tenth rib backfat 3 Maternal ** (cm) Marbling score 0 Maternal *** Loin eye area 87 Paternal * Cholesterol 119 Maternal ** Carcass length (mg/100g) 3 Maternal *** Tenth rib backfat 96 Maternal * h (cm) Ham Hunter 17 Maternal * Lactate 74 Maternal ** Tenderness score 52 Maternal **** h Loin Hunter 57 Maternal * ADG early 87 Maternal * Day weight 87 Maternal ** Glycogen 24 Paternal *** Tenth rib backfat 0 Maternal ** a * Significant (cm) ** Significant at 1% chromosome-wise level *** Significant at 5% genome-wise level **** Significant at 1% genome-wise level Estimated effects for the inferred genetic model. The effect is expressed as effect of the Berkshire allele minus the effect of the Yorkshire allele.

6 Parent-of-origin effects were also identified on SSC3 for off flavor score (Table 1), one maternally expressed and an adjacent that is paternally expressed. This could also represent a single that is partially expressed. Several with maternal expression were detected in the same marker interval in the central region of SSC9 for traits related to meat quality, including drip loss, light reflectance in the loin, and off flavor score (Table 1). Only the for off flavor score was detected under the Mendelian model. Maternally expressed were also identified for on SSC10 for tenth rib backfat and marbling in the proximal region and for cholesterol in the distal region (Table 1). A paternally expressed was identified for loin eye area in the central region. Only the for marbling was also detected using the Mendelian model. Another genomic region with multiple with parent-of-origin effects was identified in the distal region of SSC17 (Table 1), where maternally expressed were detected for 16 th day weight and average daily gain from birth to weaning (not shown). Chromosome 18 also showed parent-of-origin effects for two traits but in different regions; a paternally expressed for glycogen in the middle range of the chromosome and a maternally expressed for tenth rib backfat in the proximal region. Single parent-of-origin were identified on SSC 4, 5, 6, 11, 12, 14, and 16. Discussion and implications This study has identified several new and identified their mode of inheritance for the Berkshire x Yorkshire breed cross. Characterization of the mode of inheritance of is important to enable proper incorporation of results in selection programs in order to maximize their impact in commercial progeny. For example, as pointed out by De Koning et al. (2000), the mother of piglets has requirements for energy reserves that her offspring do not. Knowing how genes for body fat are inherited and expressed will allow breeders to derive specific crossbreeding and mating combinations to optimise the genetic constitution of animals in relation to their role in the production system (e.g. Figure 8). Figure 8. Tactical use of with parent-of-origin effects in crossbreeding, using the paternally expressed IGF-2 region as an example.

7 IGF-2 region Berkshire allele higher BF lower LEA expressed if inherited from sire Tactical use in cross breeding BB X YY YY X BY Higher BF Terminal progeny YB YY Low BF, greater LEA

8 Acknowledgements This work was made possible through financial support from an industry consortium consisting of the National Pork Board, the Iowa Pork Producers Association, the Iowa Purebred Swine Council, Babcock Genetics, Danbred USA, Monsanto Choice Genetics, PIC/Sygen, Seghers Genetics USA, and Shamrock Breeders, and by a grant from USDA/CSREES IFAFS, grant # Additional financial support was provided from the Iowa Agriculture and Home Economics Experimental Station, Ames, project no Several additional ISU faculty, staff, and students contributed to the success of this project, including Drs. Tom Baas, Lauren Christian, Steve Lonergan, Elisabeth Huff-Lonergan, Rohan Fernando, Ken Prusa, Zhiliang Hu, Daniel Ciobanu, Yang Zhang, and Peiqi Chen, and Ms. Jeanine Helm, Ms. Chris Fedler, Mr. Marlan Braet, and Mr. John Newton and personnel at the ISU Bilsland swine breeding farm. References Constancia M., B. Pickard, G. Kelsey, and W. Reik Imprinting mechanisms. Genome Research 8: De Vries, A.G., R. Kerr, B. Tier, T. Long, and T.H.E. Meuwissen Gametic imprinting effects on rate and composition of pig growth. Theor. Appl. Genet. 88: De Koning, D.J., A.P. Rattink, B. Harlizius, J.A.M. van Arendonk, E.W. Brascamp, and M.A.M. Groenen Genome-wide scan for body composition in pigs revealed important role of imprinting. Proc. Natl. Acad. Sci. USA 97: De Koning, D.J., B. Harlizius, A.P. Rattink, M.A.M. Groenen, E.W. Brascamp, and J.A.M. van Arendonk. 2001a. Detection and characterization of quantitative trait loci for meat quality traits in pigs. J. Anim. Sci. 79: De Koning, D. J., A. P. Rattink, B. Harlizius, M. A. M. Groenen, E. W. Brascamp, and J. A. M. van Arendonk. 2001b. Detection and characterization of quantitative trait loci for growth and reproduction traits in pigs. Livest. Prod. Sci. 72: De Koning, D.-J., H. Bovenhuis, and J.A.M. van Arendonk On the detection of imprinted quantitative trait loci in experimental crosses of outbred species. Genetics. 161: Georges, M., G. Andersson, M. Braunschweig, N. Buys, C. Collette, Moreau, L., Nezer, C., Nguyen, M., Van Laere, A.-S., and L. Andersson Genetic dissection of an imprinted mapping to proximal SSC2. Plant & Animal Genomes XI Conference, San Diego, W327.

9 Jeon, J.T., O. Carlborg, A. Toernsten, E. Giuffra, V. Amarger, P. Chardon, L. Andersen- Eklund, K. Andersson, I. Hansson, K. Lundstroem, and L. Andersson A paternally expressed affecting skeletal and cardiac muscle mass in pig maps to the IGF2 locus. Nat. Genet. 21: Knott S.A., L. Marklund, C.S. Haley, K. Andersson, W. Davies, H. Ellegren, M. Fredholm, I. Hansson, B. Hoyheim, K. Lundström, M. Moller, and L. Andersson Multiple marker mapping of quantitative trait loci in a cross between outbred wild boar and large white pigs. Genetics 149: Malek, M., J.C.M. Dekkers, H.K. Lee, T.J. Baas, and M.F. Rothschild. 2001a. A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. I. Growth and body composition. Mamm. Genome. 12: Malek, M., J.C.M. Dekkers, H.K. Lee, T.J. Baas, K. Prusa, E. Huff-Lonergan, and M.F. Rothschild. 2001b A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. II. Meat and muscle composition. Mamm. Genome 12: Nezer, C., L. Moreau, B. Brouwers, W. Coppieters, J. Detillieux, R. Hanset, L. Karim, A. Kvasz, P. LeRoy, and M. Georges An imprinted with major effect on muscle mass and fat deposition maps to the IGF2 locus in pigs. Nat. Genet. 21: